if you are using just windows you add the flag to a shortcut for the application. Rightclick the shortcut>properties>Target field = "C:\Program Files\iNav\iGuidance.exe" nowarning

using a button in RR the code for the button would be
RUN; "C:\Program Files\iNav\iGuidance.exe|nowarning"

using skinbedder, it uses autoIT to launch IG so you will have to edit the startup.au3 file found in the skinbedder dir (you will also need to install AutoIT3 to recompile the script to a .exe)
edit startup.au3 and edit the line
Run("C:\Program Files\iNav\iGuidance\iGuidance.exe nowarning", "C:\Program Files\iNav\iGuidance")
to look like above.

Well, whenever my system came out of Hibernation, it would throw up the error because the GPS hadn't had time to reconnect to the Sats. I also get this error whenever I am doing some testing on one of my systems because I don't have an extra GPS unit to plug in. It is just a nag, but I thought somebody else might have a work around too.